Hi everyone， I am a newer in Galaxy. I installed my Galaxy with Torque2.5.0 . I used my job_conf.xml for a test ,my Galaxy seems to work with TORQUE by the interface of pbs_modoule ( _pbs.so) successfully. In my test job_conf.xml , it seems that we should use <tools>collection of <tool id="bwa_wrapper" destination="multicorejobs4"/>to specify bwa to run as multicorejobs4. But I do not sure wheather all the tools in Galaxy we should specify their destination (such as, regularjobs,longjobs), or all the tools would work with a default destination(<destinations default="regularjobs">).,unless we specify them. Could anyone give me some help please? This is my test job_conf.xml: <?xml version="1.0"?> <job_conf> <plugins workers="4"> <!-- "workers" is the number of threads for the runner's work queue. The default from <plugins> is used if not defined for a <plugin>.--> <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="2"/> <plugin id="pbs" type="runner" load="galaxy.jobs.runners.pbs:PBSJobRunner" workers="8"/> </plugins> <handlers default="batch"> <!-- Additional job handlers - the id should match the name of a [server:<id>] in universe_wsgi.ini. --> <handler id="node01" tags="batch"/> <handler id="node02" tags="batch"/> <!-- <handler id="handler10" tags="handlers"/> <handler id="handler11" tags="handlers"/> <handler id="handler12" tags="handlers"/> <handler id="handler13" tags="handlers"/> --> </handlers> <destinations default="regularjobs"> <!-- Destinations define details about remote resources and how jobs should be executed on those remote resources. --> <destination id="local" runner="local"/> <destination id="regularjobs" runner="pbs" tags="cluster"> <!-- These are the parameters for qsub, such as queue etc. --> </destination> <destination id="longjobs" runner="pbs" tags="cluster,long_jobs"> <!-- These are the parameters for qsub, such as queue etc. --> </destination> <destination id="shortjobs" runner="pbs" tags="cluster,short_jobs"> <!-- These are the parameters for qsub, such as queue etc. --> </destination> <destination id="multicorejobs" runner="pbs" tags="cluster,multicore_jobs"> <!-- These are the parameters for qsub, such as queue etc. --> </destination> <destination id="real_user_cluster" runner="pbs"> <param id="galaxy_external_runjob_script">scripts/drmaa_external_runner.py</param> <param id="galaxy_external_killjob_script">scripts/drmaa_external_killer.py</param> <param id="galaxy_external_chown_script">scripts/external_chown_script.py</param> </destination> <destination id="dynamic" runner="dynamic"> <!-- A destination that represents a method in the dynamic runner. --> <param id="type">python</param> <param id="function">interactiveOrCluster</param> </destination> </destinations> <tools> <!-- Tools can be configured to use specific destinations or handlers, identified by either the "id" or "tags" attribute. If assigned to a tag, a handler or destination that matches that tag will be chosen at random.--> <tool id="bwa_wrapper" destination="multicorejobs"/> </tools> <limits> <!-- Certain limits can be defined.--> <limit type="registered_user_concurrent_jobs">500</limit> <limit type="unregistered_user_concurrent_jobs">1</limit> <limit type="concurrent_jobs" id="local">1</limit> <limit type="concurrent_jobs" tag="cluster">200</limit> <limit type="concurrent_jobs" tag="long_jobs">200</limit> <limit type="concurrent_jobs" tag="short_jobs">200</limit> <limit type="concurrent_jobs" tag="multicore_jobs">100</limit> </limits> </job_conf>
shenwiyn